Adam MatějGeorgetown University | GU · Department of Chemistry
Adam Matěj
Doctor of Philosophy
On-surface synthesis simulations /
Biradical conjugated molecules
About
26
Publications
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Introduction
I am a PostDoc with a focus on CompChem for conjugated molecules and materials. My main research deals with reaction mechanisms in On Surface Synthesis. I am currently expanding my expertise toward open-shell systems, namely the connection between structure and electronic structure.
Additional affiliations
September 2016 - June 2019
Publications
Publications (26)
The design of atom thick two-dimensional (2D) frameworks by on-surface synthesis has recently contributed to the development of advanced materials with high control over their structural, electronic, optical and magnetic properties. Countless 2D frameworks, with a large variety of applications, can be synthesized made of purely organic molecules (c...
Open-shell nanographenes exhibit unconventional π-magnetism arising from topological frustration or strong electron–electron interaction. However, conventional design approaches are typically limited to a single magnetic origin, which can restrict the number of correlated spins or the type of magnetic ordering in open-shell nanographenes. Here we p...
The design of supramolecular organic radical cages and frameworks is one of the main challenges in supramolecular chemistry. Their interesting material properties and wide applications make them very promising for (photo)redox catalysis, sensors, or host–guest spin–spin interactions. However, the high reactivity of radical organic systems makes the...
In the last few years we have observed a breakpoint in the development of graphene-derived technologies, such as liquid phase filtering and their application to electronics. In most of these...
The design of supramolecular organic radical cages and frameworks is one of the main challenges in supramolecular chemistry. Their interesting material properties and wide applications make them very promising for (photo)redox catalysis, sensors, or host-guest spin-spin interactions. However, the high reactivity of radical organic systems makes the...
Open-shell benzenoid polycyclic aromatic hydrocarbons, known as magnetic nanographenes, exhibit unconventional p-magnetism arising from topological frustration or strong electronic-electron (e-e) interaction. Imprinting multiple strongly entangled spins into polyradical nanographenes creates a major paradigm shift in realizing non-trivial collectiv...
The synthesis of two-dimensionally extended polycyclic heteroatomic molecules keeps attracting considerable attention. In particular, frameworks bearing planar cyclooctatetraenes (COT) moieties can display intriguing properties, including antiaromaticity. Here, we present an on-surface chemistry route to square-type porphyrin tetramers with a centr...
Here, we report a new on-surface synthetic strategy to precisely introduce five-membered units into conjugated polymers from specifically designed precursor molecules that give rise to low-bandgap fulvalene-bridged bisanthene polymers. The selective formation of non-benzenoid units is finely controlled by the annealing parameters, which govern the...
Selective activation and controlled functionalization of C-H bonds in organic molecules is one of the most desirable processes in synthetic chemistry. Despite progress in heterogeneous catalysis using metal surfaces, this goal remains challenging due to the stability of C-H bonds and their ubiquity in precursor molecules, hampering regioselectivity...
Carbon nanostructures with zigzag edges exhibit unique properties—such as localized electronic states and spins—with exciting potential applications. Such nanostructures however are generally synthesized under vacuum because their zigzag edges are unstable under ambient conditions: a barrier that must be surmounted to achieve their scalable integra...
The synthesis of novel polymeric materials with porphyrinoid compounds as key components of the repeating units attracts widespread interest from several scientific fields in view of their extraordinary variety of functional properties with potential applications in a wide range of highly significant technologies. The vast majority of such polymers...
Regiospecific C−H activation is a promising approach to achieve extended polymers with tailored structures. While a recent on‐surface synthetic approach has enabled regioselective homocoupling of heteroaromatic molecules, only small oligomers have been achieved. Herein, selective C−H activation for dehydrogenative C−C couplings of hexaazatriphenyle...
Regiospecific C‐H activation is a promising approach to achieve extended polymers with tailored structures. While a recent on‐surface synthetic approach has enabled regioselective homocoupling of heteroaromatic molecules, only small oligomers have been achieved. Herein, selective C H activation for dehydrogenative C−C couplings of hexaazatriphenyle...
The atomically precise control over the size, shape and structure of nanographenes (NGs) or the introduction of heteroatom dopants into their sp²‐carbon lattice confer them valuable electronic, optical and magnetic properties. Herein, we report on the design and synthesis of a hexabenzocoronene derivative embedded with graphitic nitrogen in its hon...
The atomically precise control over the size, shape and structure of nanographenes (NGs) or the introduction of heteroatom dopants into their sp2‐carbon lattice confer them valuable electronic, optical and magnetic properties. Herein, we report on the design and synthesis of a hexabenzocoronene derivative embedded with graphitic nitrogen in its hon...
Synthesis of polycyclic aromatic hydrocarbons containing various non-benzenoid rings remains a big challenge facing contemporary organic chemistry despite a considerable effort made over the last decades. Herein, we present a novel route, employing on-surface mechanochemistry, to synthesize non-alternant polycyclic aromatic hydrocarbon containing u...
Recently π–d conjugated coordination polymers have received a lot of attention owing to their unique material properties, although synthesis of long and defect‐free polymers remains challenging. Herein we introduce a novel on‐surface synthesis of coordination polymers with quinoidal ligands under ultra‐high vacuum conditions, which enables formatio...
The development of synthetic strategies to engineer π-conjugated polymers is of paramount importance in modern chemistry and materials science. Here we introduce a synthetic protocol based on the search for specific vibrational modes through an appropriate tailoring of the π-conjugation of the precursors, in order to increase the attempt frequency...
The on‐surface synthesis approach under UHV conditions has led us to the formation of 1D coordination π–d conjugated polymers on metal surfaces. The reaction of quinoidal ligand with different transition metals results in two distinct coordination motifs: four‐fold (Cr, Fe, Co, Ni) and two‐fold (Cu). The backbone of the Cu‐coordinated 1D chain is f...
The development of synthetic strategies to engineer pi-conjugated polymers is of paramount importance in modern chemistry and materials science. Here we introduce a theoretical and experimental synthetic paradigm based on the search for specific vibrational modes through an appropriate tailoring of the pi-conjugation of the precursors, in order to...
Graphene derivatives are promising materials for the electrochemical sensing of diverse biomolecules and development of new biosensors owing to their improved electron transfer kinetics compared to pristine graphene. Here, we report complex electrochemical behavior and electrocatalytic performance of variously fluorinated graphene derivatives prepa...
Questions
Questions (3)
Hi, I am running some transition state calculations in Gaussian on a moderate system (~50 atoms including 1 d-shell metal). For this, my method includes:
#p opt=(calcall,ts,noeigen) wb97xd/def2svp
I am trying to speed things up on shared memory paralel execution cluster by using up to 64 CPU (%nprocshared=64). The thing is, I put %mem=450GB, which based on gaussian manual for large SCF, that needs even 3N^2 words, is sufficitent for ~45 CPU. Indeed, the PBS output shows, that the calculation used only mem=76 GB, but vmem=480 GB. Also in the job logfile, the number of CPU is reduced from 64 to 41 due to ecpmxn. I see, that this is due to insufficient vmem on the system that I allocated.
My question is, is there a way, how to lower the allocated memory that gaussian asks for, if it doesn't use it? This is getting very limiting for me as this restricts the use of many CPU for larger systems.
Thanks for any hints and helps.
Hello, I am currently searching for TS's for H dissociation on adatoms. I model my systems in ONIOM (QM - molecule and adatom : MM - surface). My model chemistry is wB97XD/def2svp:amber. I tried several approaches towards TS and obviously, I encountered number of problems. The problem of multiple negative eigenvalues or non at all is ok, I just play around. But with one structure, I finally found a TS using:
#p opt=(newton,saddle=1,tight,calcall) int=ultrafine oniom=(wb97xd/def2svp:amber=softfirst) geom=connectivity
I also located the same TS using opt=(ts,tight,calcall) ...
At the end of the optimization, all six rows show converged YES with predicted change in energy in the order of E-12. Then I ran freq calculation with the same model chemistry on the optimized TS and the result shows not converged for both force and displacement, with predicted change in energy E-4.
My understanding is, that since I use calcall, I can trust the TS as being correct stationary point. The TS is really close to products' minimum, so there will be a sudden change in the curvature. I assume that Berny optimisation with analytical second derivatives converges correctly taking into account last steps, while freq takes only one step. This would make sense, since I also tried to run TS from current TS structure and Berny went downhill, until encountered none negative eigenvalues.
Is my thinking correct or am I mistaken at some (or all) point? Thanks for any help.
PS: calcall should print frequency analysis including thermochemistry at the stationary point found, but probably due to combination with oniom it's missing in the output. Using g16-B.01. It is present in calculations without oniom. Is there a workaround, e.g. some iOP?
Hello everybody,
I'm currently running some spin-polarized calculations using VASP code. If I ignore the fact, that TM exhibit low (<0.5) values for ELF (Kohout et.al. 2002), I noticed that the values on general are smaller when running spin-polarized. I checked on other examples. Can someone give me a hint why is it lower and if, could I know how much smaller the value gets?
